RBFECEdgeGathering¶
This cube gathers the MD equilibrium simulation data related to the Bound and Unbound simulations and the data from the RBFE mapper to perform relative binding affinity calculations by using NES.
- Input
Data record Stream - Streamed-in of the Bound simulation data
Data record Stream - Streamed-in of the Unbound simulation data
Data record Stream - Streamed-in of the mapper
- Output
Data Record Stream - Streamed-out of records where Bound and Unbound data has been paired to run relative binding free energy calculations.
Calculation Parameters¶
CPUs (cpu_count) type: integer: The number of CPUs to run this cube withDefault: 1 , Min: 1, Max: 128
Cube Metrics (cube_metrics) type: string: Set of metrics to be collectedChoices: cpu, disk, memory, network
Temporary Disk Space (MiB) (disk_space) type: decimal: The minimum amount of disk space in MiB (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.Default: 5120.0 , Min: 128.0, Max: 8589934592
GPUs (gpu_count) type: integer: The number of GPUs to run this cube withDefault: 0 , Max: 16
Instance Tags (instance_tags) type: string: Only run on machines with matching tags (comma separated)Default: “”
Instance Type (instance_type) type: string: The type of instance that this cube needs to be run on
max_mapper_edges (max_mapper_edges) type: integer: The max number of mapper edges to runDefault: 100
Memory (MiB) (memory_mb) type: decimal: The minimum amount of memory in MiBs (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.Default: 1800 , Min: 256.0, Max: 8589934592
Metric Period (metric_period) type: decimal: How often to sample metrics, in secondsDefault: 60Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPUDefault: 32
Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to addressDefault: 64
Spot policy (spot_policy) type: string: Control cube placement on spot market instancesDefault: ProhibitedChoices: Allowed, Preferred, NotPreferred, Prohibited, Required
Field parameters¶
Log Field (log_field) type: Field Type: String: The field to store messages to floe reportDefault: Log Field
Hardware Parameters¶
Machine hardware requirements
Memory (MiB) (memory_mb) type: decimal: The minimum amount of memory in MiBs (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.Default: 1800 , Min: 256.0, Max: 8589934592
Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to addressDefault: 64
Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPUDefault: 32
Temporary Disk Space (MiB) (disk_space) type: decimal: The minimum amount of disk space in MiB (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.Default: 5120.0 , Min: 128.0, Max: 8589934592
GPUs (gpu_count) type: integer: The number of GPUs to run this cube withDefault: 0 , Max: 16
CPUs (cpu_count) type: integer: The number of CPUs to run this cube withDefault: 1 , Min: 1, Max: 128
Instance Type (instance_type) type: string: The type of instance that this cube needs to be run on
Spot policy (spot_policy) type: string: Control cube placement on spot market instancesDefault: ProhibitedChoices: Allowed, Preferred, NotPreferred, Prohibited, Required
Instance Tags (instance_tags) type: string: Only run on machines with matching tags (comma separated)Default: “”
Metrics Parameters¶
Cube Metric Parameters
Metric Period (None) type: decimal: How often to sample metrics, in secondsDefault: 60Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
Cube Metrics (None) type: string: Set of metrics to be collectedChoices: cpu, disk, memory, network